Sibylla Bostoniensis

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Heads up, Americans! Ever wonder why human feces are not used as fertilizer in agriculture? You're about to find out!

The Situation: a Nationwide Outbreak of Cyclosporiasis

The US is having a exploding epidemic of cyclosporiasis.

A typical outbreak of cyclosporiasis in the US is usually numbered in the dozens of vicitms, and usually in a tight geographical area, or maybe some adjacent states. As of the last 36 hours, there are now more than 1,500 cases in Michigan,nearly 400 cases in New York (mostly NYC), more than 300 cases in Ohio, and cases spread across thirty one states and counting, including Alaska. (Yes, including Massachusetts.) Case counts have been skyrocketing over the last 72 hours, and the CDC's surveillance page is lagging behind the evening news.

Cyclosporiasis is a food-borne illness caused by a parasite. Cyclosporiasis is not usually fatal, but it causes pretty debilitating lower gastrointestinal illness, primarily "explosive diarrhea", which can last for weeks, even months untreated, and for some few unlucky bastards requires hospitalization. Right now 44 people are hospitalized in Michigan, the hardest hit state so far, as well as others in other states.

The Infectious Agent: Cyclospora cayetanensis

Cyclosporiasis is caused by the parasite Cyclospora cayetanensis (C. cayetanensis, or Cyclospora for short). It is a protozoa, which is a unicellular organism.

Cyclospora is transmitted through the oral-fecal route, and usually infects humans through vegetables contaminated by human feces, presumably through contact with contaminated fertilizer or irrigation, or from a sewage leak or infected workers relieving themselves in the fields.

(It can also be transmitted through contaminated drinking water, which seems unlikely in this case.)

Cyclospora infects the gastrointestinal tract and transmits through its oocysts, which are analogous to eggs, which are shed by infected individuals in their feces. Oocysts are not immediately infectious [CDC]:

the oocysts shed in the feces of infected persons must mature (sporulate) outside the host, in the environment, to become infective for someone else. This process is thought to require at least 1 – 2 weeks in favorable environmental conditions.

Because of this, it is believed that human-to-human transmission is rare or impossible. If so, this is unlike norovirus, which is also notoriously spread by the oral-fecal route and is enormously contagious. Caring for someone with cyclosporiasis should not be particularly risky. That said, the Amerian Medical Association is saying:

Hand hygiene, especially after toileting, changing diapers or caring for someone who is ill, can prevent the spread of Cyclospora

despite them repeating what the CDC said about sporulation; it's not clear that hand hygiene does prevent the spread of Cyclospora (read on), but obviously it's still a good idea for other reasons.

The present situation is complexified by the fact that Cyclospora is unusually hard to track, even when one is trying, which arguably, with federal changes to food safety and infectious disease tracking, we weren't really. Even under the older, more competent CDC, it was actually apparently unusual to manage to figure out conclusively what it was that infected people ate that was contaminated with Cyclospora. The official CDC list of outbreaks 2000-2017 (archive.org because yeah that seems to have gotten taken down in the last six days) is liberally sprinkled with "(suspected)" and "(likely)".

Things that make it hard to track include:

• The incubation period ranges from two days to two weeks, with an average of a week. It's hard for people to remember what they ate a week ago and where they got it. This makes contact tracing really, really hard.


• Apparently testing for it on food is quite challenging. The infective dose is apparently very, very low. One source I saw said it's only 12 oocysts – that's 12 individual cells spread over the whole surface of, say, a leaf of lettuce. You can see how any swab based test might easily not pick up anything at all, failing to hit the individual oocysts, and even if it does, that's not a strong signal to pick up on. Apparently there's been some recent developments in testing which may help, but I'm not sure how widely available they are.


• It can be tested for in humans by PRC test of their feces, but it is not routinely tested for. Part of what is happening right now with case numbers is that patients presenting with diarrheaic illness are belatedly being tested in light of the information that cyclosporiasis is more likely than usually believed. The CDC is advising physicians to entertain cyclosporiasis as a diagnostic possibility in such cases and that they will need to request cyclosporiasis testing specifically when writing orders. That said, I just saw a comment from a Redditor with a presumed case in Michigan that they were told at the urgent care they went to that they're now out of tests.


• That said, there's a false negative problem with testing the feces of someone with severe diarrhea: infected people may only pass oocysts episodically, as their bodies attempt to flush out the infection.


• I've also heard it said, and I don't know this is true, that because protozoa can reproduce sexually, their genetics are much less stable than those of viruses and bacteria, which in turn makes it harder to track lineages.

Historically (according to the CDC), most cyclosporiasis cases were in travelers who became infected from eating contaminated food abroad and then only came down with cyclosporiasis upon arrival in the US. That is clearly not the case with the present outbreak.

The Food Vehicles

No specific food has yet been identified as the culprit in the current outbreak. As per that list of previous US cyclosporiasis outbreaks, the usual suspects for foods responsible are basil, cilantro, raspberries, blackberries, snow peas, lettuce, bagged salad mix, and scallions (aka green onions). Also suspected are carrots and cabbage.

That said, there's a first time for everything, and it's not clear that is a comprehensive list of what Cyclospora can be transmitted by.

Cooking to 158ºF (70°C) kills Cyclospora, rendering produce contaminated with Cyclospora safe to eat.

A thing all those vegetables have in common is that they are commonly eaten raw. That may be why they have been vehicles of cyclosporiasis outbreaks in the past and other vegetables are not.

The current advice is to avoid eating any of those foods raw.

Note that pesto (basil), pico de gallo (cilantro), and cole slaw (cabbage and carrots) are typically made of raw ingredients; it is common for prepared potato salad to have scallions in it. Sometimes ice cream, gelato, and sorbet are made from fresh (raw) berries.

The Massachusetts Dept of Public Health says that peeled produce is probably fine.

The really bad news is that:

1) Cyclospora is really hard (or maybe impossible) to kill by usual sanitization methods, and

2) We only have identified one antibiotic that works on it.

Prevention

There is a bunch of "helpful" advice out there allegedly to protect yourself from Cyclospora, from a variety of health authorities including the CDC, which I can't help but notice seems to be at odds with the actual science we have, even the science the same health authorities are promulgating.

For instance, there's suggestions that scrubbing vegetables might helpfully get rid of at least some of the cyclospora and reduce the infectious load, but the FDA reports:

Although it’s unknown exactly how food and water become infected with Cyclospora, people should be aware that rinsing or washing food is not likely to remove it.

The CDC says, well... the CDC has a page about cyclosporiasis for the general public on which it says, under the "Prevention tips":

People can take the following food and vegetable handling recommendations to prevent foodborne illness related to fresh produce

"To prevent foodborne illness related to fresh produce" seems to be indicating that, despite this being a page about cyclosporiasis, this is general-purpose advice about avoiding foodborne illness related to fresh produce, and not actually information about what prevents cyclosporiasis, This does look like them weaseling.

That said, what they say is:

Wash hands with soap and water before and after handling or preparing raw fruits and vegetables.

Wash all fruits and vegetables thoroughly under running water before eating, cutting, or cooking.

Fruits and vegetables that are labeled "prewashed" do not need to be washed again at home.

Scrub firm fruits and vegetables, such as melons and cucumbers, with a clean produce brush.

Cut away any damaged or bruised areas on fruits and vegetables before preparing and eating.

Refrigerate cut, peeled, or cooked fruits and vegetables as soon as possible (within two hours).

I have no idea if any of that is effective or helpful for preventing cyclosporiasis. I absolutely do not think these are adequate to make safe contaminated foods. PBS is telling people to wash their cilantro and basil and buy whole heads of lettuce (instead of salad kits with pre-chopped lettuce), which strikes me as recklessly baseless advice. I get the impression there's no real way to wash a leaf of lettuce to make it safe: it has to just never get Cyclospora or other infectious contaminant on it in the first place.

Regarding disinifction and other infection control, the FDA (ibid) says:

What Do Restaurants and Retailers Need to Do?

Based on current information available Cyclospora may be resistant to routine chemical disinfection methods such as those using chlorine. However, restaurants and retailers should still follow basic food safety practices

Nevertheless, they also say, right below that:

What do Consumers Need to Do?

Consumers should follow these steps:

• Wash the inside walls and shelves of the refrigerator, cutting boards and countertops; then sanitize them with a solution of one tablespoon of chlorine bleach to one gallon of hot water; dry with a clean cloth or paper towel that has not been previously used.


• Wash hands with warm water and soap for at least 20 seconds before and after handling food.


• Wipe up spills in the refrigerator immediately and clean the refrigerator regularly.


• Always wash hands with hot, soapy water following the cleaning and sanitization process.


• Persons who think they might have become ill from eating potentially contaminated foods should consult their health care provider.

Yeah I don't know what the fomite transmission risk is. More concerning from my reading, I don't know that anybody else does either. If you get contaminated raspberries that don't leak outside their container, do they contaminate your fridge? I don't know if we know.

The FDA has an even more informative webpage for farmers, which says:

Cyclosporiasis is also endemic, or commonly found among, certain populations around the world[1], and was previously thought to occur only in produce grown in those regions. However, recent sample findings and outbreak investigations indicate domestic sources of C. cayetanensis. In July 2019, FDA found the first confirmed evidence of the presence of C. cayetanensis in two samples of domestically grown cilantro, and also related to outbreak cases.

[...]

Under experimental conditions, a combination of time and temperature (temperatures from 73° to 77°F for 7 – 15 days)[2] were required for C. cayetanensis [oocysts] to become infectious.

[...]

Although clinical testing for the parasite in human feces has been available since the 1970s, FDA recently improved the method for the detection of this parasite on some fresh fruits and vegetables. Traditional microbial testing (such as for fecal indicators like generic E. coli or fecal coliforms) will not identify the presence of C. cayetanensis but may help identify poor water quality, which may also be an indicator of human fecal contamination.

I think this last means, "we don't really have a Cyclospora test for produce, so maybe test for E. coli as a proxy?", but I am uncertain.

It is possible that municipal wastewater treatments may render C. cayetanensis inactive, however, some conflicting evidence also suggests that C. cayetanensis may remain viable even after wastewater is treated. Currently, little conclusive data exists on whether municipal water treatments are effective against C. cayetanensis.

Although chlorine and other antimicrobial chemical treatments are effective at reducing harmful populations of bacteria and viruses, they are not considered effective on C. cayetanensis. In countries/regions where cyclosporiasis is endemic, microfiltration, ozone, or UV treatments may be necessary to effectively decrease populations of C. cayetanensis in irrigation waters.

The Disease

The following is mostly from the CDC page for medical professionals about cyclosporiasis. I recommend it highly to you, at least until the CDC is found to be fucking up about this one too and a more reliable source of info is identified. You do not need to be a medical professional to read it. It's a free country and an open internet. Help yourself.

Presentation

How the disease presents:

Cyclospora infects the small intestine and typically causes watery diarrhea with frequent, sometimes explosive, bowel movements.

[...additional obvious symptoms elided...]

If untreated, the illness may last for a few days to a month or longer and may follow a remitting-relapsing course. Although cyclosporiasis usually is not life threatening, reported complications have included malabsorption, cholecystitis, and reactive arthritis.

Also:

Some infected persons are asymptomatic, particularly in settings where cyclosporiasis is endemic. Among symptomatic persons, the incubation period averages one week (ranging as soon as 2 days – 2 weeks or more).

Diagnosis

The CDC tells physicians:

Healthcare providers should consider Cyclospora as a potential cause of prolonged diarrheal illness [...]

Ova and parasite testing of stool for Cyclospora requires special stains or other laboratory procedures that are not routinely conducted in most U.S. laboratories.

Similarly, not all gastrointestinal polymerase chain reaction (PCR) panels include a target for Cyclospora. Therefore, when evaluating persons with symptoms consistent with cyclosporiasis, specifically request testing for this parasite. If indicated, stool specimens should also be checked for other microbes that can cause a similar illness.

Also:

Diagnosis can be difficult in part because patients who are symptomatic might not shed enough oocysts in their stool to be readily detectable by laboratory examinations. Therefore, patients might need to submit several specimens collected on different days.

Treatment

From the CDC [ibid]:

Trimethoprim-sulfamethoxazole (TMP-SMX), (sold as Bactrim,* Septra,* or Cotrim*) is the treatment of choice. The typical regimen for immunocompetent adults is:

• TMP 160 mg plus SMX 800 mg (one double-strength tablet), orally, twice a day, for 7 – 10 days. People living with HIV may need longer courses of therapy.

That links to this: Clinical Care of Cyclosporiasis, which says:

No highly effective alternatives have been identified yet for persons who are allergic to (or are intolerant of) TMP-SMX. Approaches to consider for such persons include observation and symptomatic treatment, use of an antibiotic whose effectiveness against Cyclospora is based on limited data, or desensitization to TMP-SMX. The latter approach should be considered only for selected patients who require treatment, have been evaluated by an allergist, and do not have a life-threatening allergy.

Anecdotal or unpublished data suggest that the following drugs are ineffective:

• Albendazole
• Azithromycin
• Diloxanide furoate
• Doxycycline
• Metronidazole
• Nalidixic acid
• Quinacrine
• Tetracycline
• Tinidazole
• Trimethoprim (when used as a single agent)

Although data from a small study among people living with HIV in Haiti suggested that ciprofloxacin might have modest activity against Cyclospora, substantial anecdotal experience among many immunocompetent persons suggests that ciprofloxacin is ineffective.

[...]

Treatment in Pregnancy

Trimethoprim-sulfamethoxazole (TMP-SMX) is a pregnancy category C drug. TMP-SMX should be used during pregnancy only if the potential benefit justifies the potential risk to the fetus. TMP-SMX should be avoided near-term because of the potential for hyperbilirubinemia and kernicterus in the newborn.

Pregnancy Category C: Either studies in animals have revealed adverse effects on the fetus (teratogenic or embryocidal, or other) and there are no controlled studies in women or studies in women and animals are not available. Drugs should be given only if the potential benefit justifies the potential risk to the fetus.

Treatment During Lactation

Trimethoprim-sulfamethoxazole (TMP-SMX) is excreted in breast milk. TMP-SMX generally is compatible with breastfeeding of healthy, full-term infants after the newborn period. However, TMP-SMX generally should be avoided by women when nursing infants who are premature, jaundiced, ill, or stressed, or who have glucose-6-phosphate dehydrogenase deficiency.

Treatment in Pediatric Patients

The safety of trimethoprim-sulfamethoxazole (TMP-SMX) in children has not been systematically evaluated. Use in children less than 2 months of age generally is not recommended.

Some Thoughts and Observations

So what should we do? Here's my thinking on it:

• Given the massive geographical distribution of cases in our present outbreak in th US, it sure looks like the problem is some commercial outfit that delivers the contaminated product nationwide.
  
  That suggests a way for those who want to eat raw produce to attempt to avoid a month-long trip the the bathroom: avoid eating raw produce which is distributed nationally, buy locally grown produce from small farms.
  
  That said, Mr. B. hit up the farmers market this week, and there were already substantial lines for the lettuce. This is an idea a lot of people are going to have. Expect prices to go up with demand.
  
  If fresh raw produce is important to you, maybe see if it's not too late to sign up for a CSA.


• Almost all the advice I've seen in the media and from health authorities has been about the consumer buying groceries and preparing food in their home. But it is possible that this has nothing to do with the grocery supply chain, and the contaminated food is being served by a restaurant chain or by restaurants that all use the same produce distributor. Earlier this week, some Taco Bell locations started posting signs that they were no longer serving "Lettuce, Cilantro Onion, Pico de Gallo, and Guacamole due to a nationwide recall." I don't know if they know something we don't, or if it's just an abundance of caution. Likewise, I was pointed at this discussion on Reddit's r/Michigan for people who have caught it to report what and where they ate raw produce, and it's got a lot of people in it pointing fingers at fast food, take-out, and dine-in restaurants.
  
  In any event, if the problem is in the, say, cilantro, it doens't stop being in the cilantro when the cilantro is in the enchilada plate you bought at a restaurant. You might want to make a point of thinking about what you order when you go out to eat or have delivery or catering.
  
  Speaking as someone who regularly tries to get restaurant staff to not put cilantro in my food: it may not be possible to police your plate in a restaurant. Maybe one of the things you want to do is avoid restaurant dining, unless the restaurant is explicitly taking measures not to be serving raw produce in the suspect categories.


• Obviously, produce you grow yourself is safe from cyclosporiasis, assuming you are not doing something deeply unwise with sewage, and that there's nothing wrong with your water supply.


• Boy, I hope we're right about what the possible type of produce is. There's a first time for everything.


• The history of cyclosporiasis outbreaks in the US and elsewhere seems to be linked to three sorts of foods: berries; leafy vegetables (including scallions and herbs) that grow low to the ground; and snow peas.
  
  I don't know what to make of the snow peas. The common theory about the berries is that they're hard to wash. That assumes that Cyclospora oocysts can be washed off other produce, and that washing therefore makes a difference, and, as I explained above, that's not at all established given what we know about sanitization of Cyclospora, though it is certainly possible.
  
  But the thing about low-growing leafy veggies: there's lots and lots of other things in that category than those already mentioned. Given the scale of the outbreak, it's unlikely the culprit is a comparatively uncommon or unpopular food. For instance, fresh mint is a low-growing leaf. If Cyclospora oocysts got on it, it would be pretty impossible to wash. But there's just not that many people out there eating raw mint leaves in the US. Likewise, raw spinach and raw kale are reasonably commonly eaten, but much less commonly than raw lettuce, cilantro, basil, and cabbage. It's probably one of those – but we don't actually know that.
  
  Raw asparagus has, iirc, been indicted in an outbreak, but I don't think it's popular enough to explain this one. Celery is a low-growing vegetable that is eaten raw – it's used as a raw ingredient in tuna, chicken, and potato salad, all popular cold dishes this time of year – but maybe not commonly enough to explain this, and it shows up on nobody's list of candidates, for I know not what reason.
  
  I suppose the question of what grocery store/restaurant produce you avoid comes down to your appetite for risk.
  
  Personally, I pitched all my lettuce but will be finishing eating my current supply of grocery store berries, then only replacing them with locally grown or going without. I read the label on the two pounds of potato salad I bought a few days ago and discovered it has scallions in it, so it went out in the trash.
  
  I am planning on continuing to eat raw tomatoes and peppers from the grocery store, though I am hoping the tomatoes Mr. B has been growing will ripen soon so I can swap to eating home-grown.
  
  I am thinking that fresh peaches and grapes are likely okay – nobody has indicated that they're a likely candidate – but I don't know if I want to take the risk.


• I recommend paying attention to the fact of that week-long (or more) incubation period. We're not used to thinking of food-borne illnesses working like that. You cannot offer to be the poison taster for a more vulnerable person and tell them the next day you didn't get sick so it must be fine. You cannot assume that if you ate some yesterday and didn't get sick it's fine for you to eat more of it.


• Folks on Reddit pointed out now is an excellent time to stock up on toilet paper or get a bidet. Likewise, if this outbreak continues to grow, remedies for the soreness of diarrhea may also become hard to source.

Finally, if you want some further reading on Cyclospora and cyclosporiasis, you might want to check out:

• 2024 Mar 20: preprints.org [pre-print server, academic articles not yet peer reviewed]: "Protozoan Infections Acquired from Food or Drinking Water: An Update" by Franca Rossi, Carmela Amadoro , et al.


• 2023 Jun 23: Microorganisms [peer reviewed scientific journal]: "Cyclospora cayetanensis: A Perspective (2020–2023) with Emphasis on Epidemiology and Detection Methods" by by Sonia Almeria, Leonor Chacin-Bonilla, et al.

That latter article is but one article in a whole special issue of Microorganisms wholly dedicated to Cyclospora cayetanensis and Cyclosporiasis.

P.S. One of the best sources I've found for breaking news about this as well as other infectious disease outbreaks is Reddit's r/ContagionCuriosity where there's a Megathread for this outbreak. As always, Your Local Epidemiologist is good for commentary on public health.